[2018-10-13 18:04:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:04:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:04:15] Checking for Bowtie index files (genome)..
[2018-10-13 18:04:15] Checking for reference FASTA file
[2018-10-13 18:04:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:04:19] Reading known junctions from GTF file
[2018-10-13 18:04:24] Preparing reads
	 left reads: min. length=100, max. length=100, 358278 kept reads (208 discarded)
	right reads: min. length=100, max. length=100, 357943 kept reads (543 discarded)
[2018-10-13 18:04:39] Building transcriptome data files /scratch/8793426.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:05:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:13:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:14:27] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:14:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:14:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:15:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:15:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:15:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:15:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:16:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:16:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:16:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:16:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:16:51] Searching for junctions via segment mapping
[2018-10-13 18:19:33] Retrieving sequences for splices
[2018-10-13 18:21:39] Indexing splices
[2018-10-13 18:21:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:22:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:22:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:22:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:22:17] Joining segment hits
[2018-10-13 18:24:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:24:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:24:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:24:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:24:58] Joining segment hits
[2018-10-13 18:27:24] Reporting output tracks
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[2018-10-13 18:30:47] A summary of the alignment counts can be found in /scratch/8793426.1.linga/tophat2/align_summary.txt
[2018-10-13 18:30:47] Run complete: 00:26:32 elapsed